Zebrafish has been widely used in biomedical experiments. However, the injection of zebrafish larvae is complicated due to their small sizes and large variations. In this paper, an automatic high-throughput microinjection system dedicated to batch injection of zebrafish larvae is designed and developed for the first time. The specially designed microarray petri dish combined with machine vision feedback enables high-efficiency automatic identification and injection of zebrafish larvae. The feasibility of the system is proved by conducting a series of experiments. The experimental results show that the system works fast and ensures stable success rate and survival rate for the microinjection. The system can be used in various biomedical experiments of zebrafish injection to liberate the experimenter from manual operation. It can improve the experimental efficiency, and hence provides a fast and stable injection way for inexperienced experimenters.